Mercurial > repos > iuc > hal_halupdatebranchlengths

comparison hal_halUpdateBranchLengths.xml @ 0:8f8634a2320b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
author iuc
date Fri, 06 Feb 2026 10:39:02 +0000
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-1:000000000000 0:8f8634a2320b
1 <tool id="hal_halupdatebranchlengths" name="halUpdateBranchLengths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>updates the branch lengths of a tree</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## Copy input HAL to ensure that it is not modified.
10 cp '$input_hal' writable_hal.hal &&
11 halUpdateBranchLengths
12 writable_hal.hal '$newickTree' &&
13 ## echo 'ok' to check it with assert_stdout. This is needed because there is no other stdout output,
14 ## and the output HAL file checksum always changes even with identical inputs.
15 echo 'ok'
16 ]]></command>
17 <inputs>
18 <expand macro="input_hal"/>
19 <param name="newickTree" type="text" value="" label="Newick Tree" help="Newick tree (must be identical, except for the branch lengths)">
20 <expand macro="sanitizer_default"/>
21 <expand macro="validator_newick"/>
22 </param>
23 </inputs>
24 <outputs>
25 <data name="out_file" format="hal" label="${tool.name} on ${on_string}" from_work_dir="writable_hal.hal"/>
26 </outputs>
27 <tests>
28 <test expect_num_outputs="1">
29 <param name="input_hal" value="halTest.hal"/>
30 <param name="newickTree" value="(Genome_1:2,Genome_2:2,Genome_3:1)Genome_0;"/>
31 <output name="out_file" ftype="hal">
32 <assert_contents>
33 <has_size min="50000"/>
34 </assert_contents>
35 </output>
36 <assert_stdout>
37 <has_line line="ok"/>
38 </assert_stdout>
39 </test>
40 </tests>
41 <help><![CDATA[
42 halUpdateBranchLengths updates the branch lengths stored in a HAL alignment using values provided by a given external Newick tree.
43 The topology of the Newick tree must exactly match the topology of the tree already stored in the HAL file.
44 Only branch lengths are replaced.
45
46 A new HAL file is created as output instead of modifying the input HAL file.
47 ]]></help>
48 <expand macro="citation"/>
49 <expand macro="creator"/>
50 </tool>